TL;DR use only one screen and they work.
I have a potential fix for this! I have 2 screens (internal laptop monitor, and external monitor). I noticed that the problem only presents when I’m using “dual monitor” mode and have “gallery view” enabled. The controls also don’t appear if I have “full screen” enabled. They also won’t appear if I have either window on the external monitor.
It works in “dual monitor” mode if I have the controls window set to “speaker view” and not in “full screen” with both windows on the internal (laptop) monitor. I can then move either window to the external monitor. If I’ve accidentally started Annotation mode “wrong”, I have to cancel it and move all windows to the internal monitor before re-starting Annontation mode.
I have my controls back! This is with version 5.2.458699.0906 1
I have version 5.3.47…. (no way to copypaste) and they don’t, but using only one monitor helped. Though I get a black screen underneath annotations when/as I’m writing them.